Growth of microorganism in the membrane distillation (MD) system has been evaluated, and their presence on the membrane surface was studied using scanning electron microscopy (SEM) coupled with energy dispersion spectrometry (EDS). The membrane samples were collected from MD modules used for the following applications: concentration of salts and acids, production of demineralized water from tap water, separation of ethanol from fermentation broth in a membrane bioreactor and treatment of saline wastewater containing Pseudomonas and Streptococcus faecalis bacteria and Penicillium and Aspergillus fungi. The MD experiments were performed with polypropylene capillary membranes. SEM examinations of the membranes used for the treatment of saline wastewater indicated a significant amount of S. faecalis bacteria and Aspergillus fungi. The polypropylene membranes used did not reject S. faecalis bacteria, which were detected on the membrane surface on the distillate side. The presence of fungi in the membrane pores was observed only on the feed side. The contamination of the membrane surface by yeast cells was not observed in the case of the membrane bioreactor operated over one year. The running conditions of the MD process (such as elevated temperature, significant salt concentrations and low pH values) inhibited the growth of microorganism in the MD system.